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Indian forces surrounded the mosque after two soldiers were killed in an exchange of fire with the suspected separatists.
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The Indians said two suspects were killed while attempting to escape out of the mosque's windows.
A military spokesman says the army used only small arms in an attempt to avoid damaging the mosque, but that an explosion took place inside the building.
However it is not clear what, if any, damage was caused.
Sanctuary
The BBC correspondent in Srinagar, Altaf Hussain, says places of worship have rarely been involved in the 10-year Kashmir conflict, and the authorities are worried that Muslim sentiments might be inflamed if the mosque is damaged.
Nearly a dozen militant groups are fighting Delhi's rule in Kashmir, where police and hospitals say more than 25,000 people have been killed in a decade of violence.
The fighters have previously used mosques and Islamic shrines as sanctuaries.
In 1993, Indian troops besieged a lakeside shrine in Srinagar after militants took over the building, sparking anti-India protests in the Muslim-majority region.
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